@Themus - it would rather help if you told us what version of Sigil you were using and your OS... if you are using the 0.5.90x betas, then report it on the beta thread describing exactly your steps to reproduce it.

If you are using one of the earlier versions (like 0.5.3 or earlier) then yes there are various synchronisation bugs in the code. These have been fixed for the 0.5.90x beta builds, unless you have managed to find a new edge case for it (hence why we would need exact repro steps).